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Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya

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Otieno, Grieven P., Murunga, Nickson, Agoti, Charles N., Gallagher, Katherine E., Awori, Juliet O. and Nokes, D. James (2020) Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya. Wellcome Open Research, 5 . 150. doi:10.12688/wellcomeopenres.16037.2

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Official URL: http://dx.doi.org/10.12688/wellcomeopenres.16037.2

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Abstract

Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya.
Methods: Continuous surveillance of pneumonia admissions was conducted at the Kilifi county hospital (KCH) located in the northern coastal region of Kenya. Children aged <5 years admitted to KCH with clinically defined syndromic severe or very severe pneumonia were recruited. Respiratory samples were taken and tested for 15 virus targets, using real-time polymerase chain reaction. Unadjusted odds ratios were used to estimate the association between demographic and clinical characteristics and HCoV positivity.
Results: From 2007 to 2019, we observed 11,445 pneumonia admissions, of which 314 (3.9%) tested positive for at least one of the HCoV types surveyed in the study. There were 129 (41.1%) OC43, 99 (31.5%) 229E, 74 (23.6%) NL63 positive cases and 12 (3.8%) cases of HCoV to HCoV coinfection. Among HCoV positive cases, 47% (n=147) were coinfected with other respiratory virus pathogens. The majority of HCoV cases were among children aged <1 year (66%, n=208), though there was was no change in the proportion infected by age. HCoV-OC43 was predominant of the three HCoV types throughout the surveillance period. Evidence for seasonality was not identified.
Conclusions: Overall, 4% of paediatric pneumonia admissions were associated with three endemic HCoVs, with a high proportion of cases co-occurring with another respiratory virus, no clear seasonal pattern, and with the age-distribution of cases following that of pneumonia admissions (i.e. highest in infants). These observations suggest, at most, a small severe disease contribution of endemic HCoVs in this tropical setting and offer insight into their potential future burden and epidemiological characteristics.

Item Type: Journal Article
Subjects: Q Science > QR Microbiology > QR355 Virology
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Coronaviruses, Pneumonia in children -- Kenya, Pneumonia
Journal or Publication Title: Wellcome Open Research
Publisher: F1000Research
ISSN: 2398-502X
Official Date: 22 September 2020
Dates:
DateEvent
22 September 2020Available
22 September 2020Accepted
26 June 2020Available
Volume: 5
Article Number: 150
DOI: 10.12688/wellcomeopenres.16037.2
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
102975Wellcome Trusthttp://dx.doi.org/10.13039/100010269
220985Wellcome Trusthttp://dx.doi.org/10.13039/100010269
48968 Bill and Melinda Gates Foundationhttp://dx.doi.org/10.13039/100000865
UNSPECIFIEDJohns Hopkins University. School of Hygiene and Public Healthhttp://viaf.org/viaf/151152313
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